Saturday, 28 December 2013

How do we define fossil species?

How do we define fossil species?

What do we currently understand by a 'species'?

Naming species, also known as alpha taxonomy, forms the fundamental basis and core of systematic analysis (e.g., for biodiversity, macroevolutionary and ecological studies). Since the origin of the species concept, there has been heated and continuous debate as to what exactly constitutes a species. The discovery of DNA as an evolutionary tool sparked a vigorous new line of discussion into what defines a species. Even to this day, despite a wealth of theoretical, empirical and philosophical studies, there is still a lack of consensus in the way of rigorously defining a species unit. This is not to say that there isn't a general idea of what a species is (ask any biologist or palaeontologist); in fact most people reading this will probably have a pretty good idea of what they define a species as. But there is not total agreement, not by a long shot. Furthermore, most if not all current species concepts are explicitly based on extant organisms based directly on observations and data from their every day life, and whom also just happen to provide a near-endless supply of tasty DNA. But what about fossils? Using fossils in conjunction with systematic analysis is vital, and their exclusion a violation of the principles of science (which unfortunately is all too frequent). But how do palaeontologists actually recognise and diagnose fossil species? This is a pretty serious issue, considering that DNA of fossil organisms has almost always decayed long before exhumation, and fossil remains typically only represent a biased sample of the organism it once was.

What are the current species concepts?

For biologists, the 'species problem' can be framed as: “What level of divergence (morphological, genetic, etc.) between populations constitutes independent species diagnosis?” This can be modified slightly according to whichever species concept and parameter is being applied (see below). Using DNA as a sole basis for species delimitation is fraught with issues, including but not limited to the concept of paralogy, lateral gene transfer (transfection), arbitrary delimitation protocols, lack of data (e.g., in tropical species), and often a lack of training or instrumentation (in third world countries mainly). It is currently widely accepted that a combined approach using both morphological and molecular data is the most rigorous method to assess species' validity. In spite of this, and a continuous refinement and development of technqiues, there is no single 'silver bullet' method for delimiting species (although many DNA taxonomists will try and pretend there is..). What we actually have are a series of non-independent concepts that actually apply to different stages of the process of speciation, or population divergence (de Quieroz 2007 discusses this in a most brilliant manner). Here are a couple of examples of current concepts:

  • Biological Species Concept: This is the one most people will have heard of. Species are defined by reproductive isolation, or the ability to produce fertile offspring. Obvious issues with this are if you're asexual, and how do you know if two organisms (within reason) can or cannot mate if they are not sympatric. Moreover, reproductive isolation is not always congruent with morphological or genetic divergence. Fossils cannot be diagnosed.

  • Phylogenetic Species Concept: This refers to diagnosability based on the monophyly of a population. This invariably invokes the use of DNA. Genetic population divergence goes through three stages: polyphyly, paraphyly and finally reciprocal monophyly, giving two or more irreducible clusters of diagnosable organisms with a traceable pattern of ancestry and descent. Fossils cannot be diagnosed.

  • Genealogical Species Concept: This is the use of multiple gene marker distributions to delimit putative species by identifying periods of complete lineage sorting. Essentially this means that the incongruence from coalescence (the point in time where gene variants unite in a gene genealogy) no longer affects delimitation. Unsurprisingly, fossils can't be diagnosed.

Throughout all of these concepts, sampling remains an issue. How do you know if that your analyses are showing you is the product of a true biological signal, or just chance occurrence based on the individuals tested?

A currently widely used method of delimitation is DNA barcoding. Some molecular systematists deem this as a powerful enough tool to entirely replace standard Linnaean taxonomy, although (obviously) there are numerous vocal objections. DNA barcoding operates on the assumption that there is a threshold for species delimitation based on a single gene, which is the entirely arbitrary 10-times-greater genetic divergence (interspecific) than intraspecificity, leading to the concept of reciprocal monophyly. It works sometimes, but is fraught with theoretical and empirical problems. (I love the idea that molecular systematists will go to the tropics with the aim of identifying unique or diverse haplotypes in insects etc., by killing as many organisms as possible; “We've found a unique haplotype! We must therefore preserve this beetle at all costs!”, as the decapitated beetle floats around the dissection palate..)

How do these concepts relate to fossils?

Every single one of these concepts rely on either direct observational data (e.g., sympatry for the BSC), or the use of DNA. Few modern studies rely solely on morphology to delimit species (annoyingly, seeing as it is directly coupled with behaviour, ecology etc.; DNA is just, well, DNA..). So really, with regards to fossils, in which phenotype is the only aspect preserved (and ecology etc. accordingly inferred), as well as the spatio-temporal context in which it exists, how can these concepts be applied? Well, they can't really. So what can palaeontologists do..?

How are fossil species delimited?

In principle, there are two different methods of species delimitation: a discovery-based approach, and a hypothesis-based approach. The former makes no a priori assumptions regarding the putative species in a sample, only delimiting subsequent to analysis (e.g., DNA barcoding, cladistics). The latter requires an a priori assumption of what species already exist within a sample, with the analysis being a validation test. It varies in papers as to whether a full or partial cladistic analysis is carried out (if at all) when the focus if the paper is the erection and description of a new species. By partial analysis, I simply mean that the authors observe the synapomorphies of a specific clade and see if their specimen(s) match or not. This is a pretty horrendous breach of taxonomy and cladistic methodology, as it ignores the fact the every single character placement and it's polarity is influenced by the addition of new species (in fact, this is the principal method by which cladograms are initially constructed). Full analysis is the dominantly used method, thankfully, given the accessibility of free software and relative simplicity in executing cladistic analysis (although there may be issues in obtaining and extracting previous data sets, but that's another tale too. For someone else). This leads us on to the next part.

Bring on Cladistics

Cladistics is the method that sytematists use to forge a hierarchical grouping of taxa into discrete subsets, or clades, for the inference of common ancestry between species and groups. A clade is defined by a node (or sometimes a branch) - the point of intersection of two or more branches - that represents the common ancestry and speciation event of all subsequent taxa. Each node is represented by one or more shared derived characters (synapomorphies) between all branches, and hence taxa, emanating from the node. If the taxa in question are species (i.e., terminal branches), then the minimum required number of synapomorphies to give a sister taxa relationship is one, and the minimum number of required autapomorphies (unique derived characters) to 'split' the branch into two separately recognised entities, is one. That is, cladistics can recognise discrete units, including species, on the basis of a single unique character, regardless of the size of the initial character set. There are statistical methods of assessing the strength or support of this (e.g., pseudo-replication analyses, branch decay tests), but the point remains that a species can be delimited through cladistic analysis based on the possession of a single unique character. [this is a really simple overview, there are numerous web-pages and texts out there that describe cladistic methodology in more detail; just search.]

It seems that there are two main methods of delimiting fossil species: qualitatively, whereby the fossil simply looks different but the differences are not broken down into discrete characters; and quantitatively, where the species name is supported by x number of autapomorphies, and the strength or support of the diagnosis is a function of x, and is testable through cladistic methods. This is pretty much the only method available to palaeontologists given the relative paucity of fossil data. But then how many autapomorphies are required to be interpreted as a 'strong', or valid, diagnosis? And to what extent are species therefore comparable? It's a problematic issue, that I haven't actually came across much at all in the published literature. If I'm mistaken, please do point me in the right direction! What is perhaps required though, is a rigorous species concept that is directly compatible with the full range of fossil diversity, and that extant taxa can be integrated in to. More advanced methods than cladistics do exist, such as Maximum Likelihood and Bayesian analyses which rely on probability estimates and high parameter models. Unfortunately, these methodswere developed with the high quantity of data generated from DNA seuqencing in mind, and the theoretical basis for applying the models to morphological data remains elusive (not that this stops a lot of people from doing it anyway).

[Picture of diverse Ammonites]

With so many different forms, how do we confidently draw boundaries between different varieties?

One thing to consider is that species are treated as discrete entities when these concepts are applied; is this the correct approach when really a lineage on which an organism sits is by definition, continuous? What do we gain by stamping an arbitrary and highly subjective boundary on this continuum? A method of classification. It has heuristic value in systematics, but it seems that the fundamental treatment of species as discrete units may need some consideration. Furthermore, speciation is a pretty stochastic and deterministic process, and the application of delimitation criteria must be flexible to account for the variation between lineages.

What is undoubtedly required in the future is the development of a theoretical and empirical basis for species delimitation, based on all valid sources of data required. Such a holistic approach however is problematic due to the dificulties in consistency between data sets, and the difficulty in obtaining them initially in the first place. There are additional issues too such as sampling biases, which are being resolved concurrently with the research into species identification, which ultimately is requiring a global cross-disciplinary approach. In spite of the effort though, the future of species definitions in palaeontology lacks clarity, but still forms the basis for almost all research.

As a final consideration, wiith respect to all of the work that has gone into validating 'species', what has been done to test the validity of higher taxonomic units, such as Family and Order, or even the Genus? It's worth pondering about what these mean in the context of systematic biology

Creationist comment:

The problem which evolutionist palaeontologists on the palaeocritti team admit being one, is a field where Creationists have done independent research, so called Baraminology. From Hebrew bara - create - and min - kind. See for instance the articles:

A baraminology tutorial with examples from the grasses (Poaceae)
by Todd Charles Wood

Molecular limits to natural variation
by Alex Williams

A specific critique about palaeontological cladistics is the accusation of splitting species and genera too much.

Dino ‘puberty blues’ for paleontologists
Dinosaur juveniles and adults wrongly labelled as separate species
by David Catchpoole

Too many dinosaur names
by David Catchpoole

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